AIMC Topic: Polymorphism, Single Nucleotide

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Bi-stream CNN Down Syndrome screening model based on genotyping array.

BMC medical genomics Nov 20, 2018
BACKGROUND: Human Down syndrome (DS) is usually caused by genomic micro-duplications and dosage imbalances of human chromosome 21. It is associated with many genomic and phenotype abnormalities. Even though human DS occurs about 1 per 1,000 births wo...
Down Syndrome Chromosome Mapping Neural Networks, Computer Deep Learning Polymorphism, Single Nucleotide Genotype Humans
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A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data.

Nature genetics Nov 5, 2018
Cancer genomic analysis requires accurate identification of somatic variants in sequencing data. Manual review to refine somatic variant calls is required as a final step after automated processing. However, manual variant refinement is time-consumin...
DNA Mutational Analysis Electronic Data Processing Polymorphism, Single Nucleotide Sequence Analysis, DNA Humans Reproducibility of Results Mutation Software Neoplasms High-Throughput Nucleotide Sequencing Deep Learning Algorithms Computer Simulation
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Effective feature learning and fusion of multimodality data using stage-wise deep neural network for dementia diagnosis.

Human brain mapping Nov 1, 2018
In this article, the authors aim to maximally utilize multimodality neuroimaging and genetic data for identifying Alzheimer's disease (AD) and its prodromal status, Mild Cognitive Impairment (MCI), from normal aging subjects. Multimodality neuroimagi...
Humans Female Cognitive Dysfunction Dementia Polymorphism, Single Nucleotide Multimodal Imaging Neuroimaging Aged Male Middle Aged Deep Learning
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Ensemble of machine learning algorithms using the stacked generalization approach to estimate the warfarin dose.

PloS one Oct 19, 2018
Warfarin dosing remains challenging due to narrow therapeutic index and highly individual variability. Incorrect warfarin dosing is associated with devastating adverse events. Remarkable efforts have been made to develop the machine learning based wa...
International Cooperation Humans Linkage Disequilibrium Machine Learning Thrombosis Medical Errors Polymorphism, Single Nucleotide Vitamin K Epoxide Reductases Hemorrhage Genotype Algorithms Drug Administration Schedule Aged, 80 and over Anticoagulants Middle Aged Multivariate Analysis Databases, Factual Warfarin Male Pharmacogenetics Female Cohort Studies Aged
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PBMDR: A particle swarm optimization-based multifactor dimensionality reduction for the detection of multilocus interactions.

Journal of theoretical biology Oct 5, 2018
Studies on multilocus interactions have mainly investigated the associations between genetic variations from the related genes and histopathological tumor characteristics in patients. However, currently, the identification and characterization of sus...
Female Breast Neoplasms Genetic Predisposition to Disease Polymorphism, Single Nucleotide Genotype Humans Algorithms Genetic Loci Multifactor Dimensionality Reduction Genes, Neoplasm
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A universal SNP and small-indel variant caller using deep neural networks.

Nature biotechnology Sep 24, 2018
Despite rapid advances in sequencing technologies, accurately calling genetic variants present in an individual genome from billions of short, errorful sequence reads remains challenging. Here we show that a deep convolutional neural network can call...
DNA Mutational Analysis Neural Networks, Computer Genome, Human Software INDEL Mutation Animals Sequence Analysis, DNA Humans Genomics Polymorphism, Single Nucleotide Mammals Genotype High-Throughput Nucleotide Sequencing
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Detecting gene-gene interactions for complex quantitative traits using generalized fuzzy classification.

BMC bioinformatics Sep 18, 2018
BACKGROUND: Quantitative traits or continuous outcomes related to complex diseases can provide more information and therefore more accurate analysis for identifying gene-gene and gene- environment interactions associated with complex diseases. Multif...
Polymorphism, Single Nucleotide Computational Biology Models, Genetic Fuzzy Logic Genetic Markers Epistasis, Genetic Phenotype Female Animals Mice Humans
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Using recursive feature elimination in random forest to account for correlated variables in high dimensional data.

BMC genetics Sep 17, 2018
BACKGROUND: Random forest (RF) is a machine-learning method that generally works well with high-dimensional problems and allows for nonlinear relationships between predictors; however, the presence of correlated predictors has been shown to impact it...
Humans Machine Learning Genome-Wide Association Study Polymorphism, Single Nucleotide CpG Islands Triglycerides Hypertriglyceridemia Genotype Epigenomics Hypoglycemic Agents DNA Methylation
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Serum vitamin D deficiency and vitamin D receptor gene polymorphism are associated with increased risk of cardiovascular disease in a Chinese rural population.

Nutrition research (New York, N.Y.) Sep 13, 2018
Several studies have reported a conflicting association between vitamin D deficiency, vitamin D receptor (VDR) polymorphism, and the risk of cardiovascular disease (CVD). We hypothesized that serum 25(OH)D concentrations and single nucleotide polymor...
Gene Frequency China Adult Triglycerides Logistic Models Blood Glucose Vitamin D Deficiency Male Humans Polymorphism, Single Nucleotide Alleles Rural Population Cardiovascular Diseases Biomarkers Genotype Asian People Vitamin D Middle Aged Female Haplotypes Receptors, Calcitriol Aged
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Utilizing Deep Learning and Genome Wide Association Studies for Epistatic-Driven Preterm Birth Classification in African-American Women.

IEEE/ACM transactions on computational biology and bioinformatics Sep 3, 2018
Genome-Wide Association Studies (GWAS) are used to identify statistically significant genetic variants in case-control studies. The main objective is to find single nucleotide polymorphisms (SNPs) that influence a particular phenotype (i.e., disease ...
Deep Learning Genome-Wide Association Study Polymorphism, Single Nucleotide Computational Biology Pregnancy Female Infant, Newborn Premature Birth Black or African American Epistasis, Genetic Humans Algorithms
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